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[PRE REVIEW]: PhenoFeatureFinder: a python package for linking developmental phenotypes to omics features #6846

Open editorialbot opened 3 months ago

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@petrableeker<!--end-author-handle-- (Petra Bleeker) Repository: https://github.com/BleekerLab/PhenoFeatureFinder Branch with paper.md (empty if default branch): Version: v0.1.1 Editor: !--editor-->@jromanowska<!--end-editor-- Reviewers: Pending Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb/status.svg)](https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb)

Author instructions

Thanks for submitting your paper to JOSS @petrableeker. Currently, there isn't a JOSS editor assigned to your paper.

@petrableeker if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 3 months ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (588.2 files/s, 389224.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              8              0              0          18840
Python                           7            505           1201           1055
Markdown                        13            164              0            290
Jupyter Notebook                 6              0           3796            252
TeX                              1             14              0            227
TOML                             1              4              0             30
DOS Batch                        1              8              1             27
YAML                             2              3              7             27
make                             1              4              5             10
-------------------------------------------------------------------------------
SUM:                            40            702           5010          20758
-------------------------------------------------------------------------------

Commit count by author:

    79  LissyDenkers
    32  Marc Galland
    10  Lissy Denkers
     1  Petra Bleeker
     1  semantic-release
editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1232

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf.

LissyDenkers commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf.

LissyDenkers commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 3 months ago

@petrableeker thanks for this submission. I am the AEiC on this track and here to help with initial steps. I am currently reviewing if this work is in scope for JOSS. In particular given the relatively small size of the project I've just flagged this for scope review by our board, to see this conforms to our substantial scholarly effort criteria. This scope review should take about 2 weeks to complete.

Kevin-Mattheus-Moerman commented 2 months ago

@petrableeker I've just removed the query-scope label as I'm pleased to confirm that this submission has passed the initial scope review process. We will now be looking for a handling editor.

Kevin-Mattheus-Moerman commented 2 months ago

@petrableeker currently all editors in this space are busy handling other submission. I've hence assigned the waitlisted label. This will help ensure you will be next once an editor becomes available.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot invite @jromanowska as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 2 months ago

@petrableeker The editor I've just invited is actually unavailable for the moment. So we will have to leave this waitlisted for the moment. Apologies for the delay and thanks for your patience. I will continue to look for an editor or, once @jromanowska becomes available she may pick this up. I'll keep you up to date.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot assign @jromanowska as editor

editorialbot commented 2 months ago

Assigned! @jromanowska is now the editor

Kevin-Mattheus-Moerman commented 2 months ago

@petrableeker I've just assigned Julia as she agreed to be editor. However, due to the summer holiday period it may take a while for her to be able to pick this up.

jromanowska commented 1 month ago

Hi everyone! I'm just back from holidays and will go on with this submission now. Thank you for your patience.

jromanowska commented 1 month ago

@editorialbot check repository

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (589.5 files/s, 389841.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              8              0              0          18840
Python                           7            505           1201           1055
Markdown                        13            165              0            292
Jupyter Notebook                 6              0           3776            252
TeX                              1             14              0            227
TOML                             1              4              0             30
DOS Batch                        1              8              1             27
YAML                             2              3              7             27
make                             1              4              5             10
-------------------------------------------------------------------------------
SUM:                            40            703           4990          20760
-------------------------------------------------------------------------------

Commit count by author:

    84  LissyDenkers
    32  Marc Galland
    10  Lissy Denkers
     1  Petra Bleeker
     1  semantic-release
editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1235

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: Other (Check here for OSI approval)

jromanowska commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 1 month ago

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

jromanowska commented 1 month ago

Hi, @petrableeker , I've just read the paper and have one comment: I find that the headers for "Summary" and "Statement of need" don't really match the content. I'd suggest headers like "Statement of need" and "Implementation" instead.

Also - do you have any suggestions for (or oppositions) reviewers? Above, our robot has suggested some names, so I'll probably choose some of them, but just wanted to know if you have any comments on this.

jromanowska commented 4 weeks ago

:wave: @msabrysarhan, @adamyhe, @coughls, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

adamyhe commented 3 weeks ago

Hi @jromanowska. I'm unfortunately rather swamped at the moment. I don't think I'll be able to review.

jromanowska commented 3 weeks ago

Hi @jromanowska. I'm unfortunately rather swamped at the moment. I don't think I'll be able to review.

@adamyhe OK, thanks, maybe next time! Do you have anyone you could recommend to be a reviewer on this one?

jromanowska commented 1 week ago

@petrableeker, @LissyDenkers - do you have any reviewer suggestions? I'm a bit stuck here.

LissyDenkers commented 4 days ago

Hi @jromanowska, So far, we could not yet find anyone. One of the authors suggested that Pablo Lopez-Tarifa (lopeztarifa on GitHub) might be able to help us. In the meantime, I'll continue searching.

jromanowska commented 4 days ago

@lopeztarifa :wave: - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html